For developers
This page is for developers who want to improve or customize OpenMebius2. The source code of OpenMebius2 is available on GitHub.
Development environment
To set up a development environment, you need to have the following software installed:
- MATLAB R2025a or later
- MATLAB Optimization Toolbox
- MATLAB Statistics and Machine Learning Toolbox
- MATLAB Parallel Computing Toolbox (optional, for parallel processing)
- MATLAB Compiler (optional, for creating standalone applications)
Data structure
Model instance
The model instance is a MATLAB structure that contains the following fields:
| Field Name | Type | Description |
|---|---|---|
tableInfo |
5×2 table | A table containing model information loaded from an Excel file. |
tableModel |
N×3 table | A table containing reactions loaded from an Excel file (N: reaction). |
tableMS |
N×3 double | A table containing atom transition loaded from an Excel file (N: reaction). |
tableBiomass |
N×2 table | A table containing biomass demands loaded from an Excel file (N: The number of biomass). |
tableXY |
N×2 table | A table containing positions of nodes in the metabolic pathway (N: The number of nodes). |
tableAtom |
N×M table | A table containing the number of atoms in each element (N: reaction, M: element). |
fileTypeModel |
string | Model file type (e.g., "xlsx"). |
fileTypeLabel |
string | File type of label pattern information (e.g., "json"). |
fileTypePathway |
string | File type of pathway map (default: "tiff"). |
fileModel |
string | Filename of the model file (default: "metabolic_network"). |
fileLabel |
string | Filename of the label pattern information (default: "label"). |
filePathway |
string | Filename of the pathway map (default: "metabolic_pathway"). |
modelRxn |
N×4 table | A table containing reaction information (N: reaction). |
modelTrans |
N×3 table | A table containing atom transition information (N: reaction). |
MSRxn |
N×3 table | A table containing reaction information for mass spectrometry (N: reaction). |
MSTrans |
N×3 table | A table containing atom transition information for mass spectrometry (N: reaction). |
Details of tables
modelRxnfields:Properties.RowNames: Reaction IDs (string)Reactants: Cell array of reactant names (1xK cell, K: number of reactants)Products: Cell array of product names (1xL cell, L: number of products)Reversible: Logical value indicating if the reaction is reversible (true/false)Independent: Logical value indicating if the reaction is designated as independent (true/false)
modelTransfields:Properties.RowNames: Reaction IDs (string)Reactants: Cell array of reactant atom patterns (1xK cell, K: number of reactants)Products: Cell array of product atom patterns (1xL cell, L: number of products)Reversible: Logical value indicating if the reaction is reversible (true/false)
MSRxnfields:Properties.RowNames: Fragment name (string)Reactants: Cell array of reactant names (1xK cell, K: number of reactants)Products: Cell array of product names (1xL cell, L: number of products)Reversible: Logical value indicating if the reaction is reversible (true/false)
MSTransfields:Properties.RowNames: Fragment name (string)Reactants: Cell array of reactant atom patterns (1xK cell, K: number of reactants)Products: Cell array of product atom patterns (1xL cell, L: number of products)Reversible: Logical value indicating if the reaction is reversible (true/false)